search

berkeleybop / bbop-graph

General purpose (mathematical) graph library in JavaScript.
BSD 3-Clause "New" or "Revised" License
2 stars 4 forks source link

Document how to programmatically visualize a bbop-graph #4

Open cmungall opened 8 years ago

cmungall commented 8 years ago

This is stale: http://wiki.geneontology.org/index.php/AmiGO_2_Manual:_Visualize_Freeform

This doesn't work visualize

Motivation: https://github.com/monarch-initiative/monarch-app/issues/1232#issuecomment-209572296

kltm commented 8 years ago

Put this in the AmiGO tracker--AmiGO's visualize is completely unrelated to bbop-graph.

kltm commented 8 years ago

Ah, more context from the other ticket.

This ticket is now to document visualizing bbop-graph. Could you add the JSON you're trying to this ticket? As well, take a look at the docs, I think you want to be looking at "graph_data".

cmungall commented 8 years ago

The JSON is in the Monarch ticket

But this ticket is about a more general issue. We have an awesome graph format, with an even more awesome ecosystem of libraries and services around it. The README should have a small collection of links to help orient people: what is a bbop-graph, what things spit them out, what things consume them? The README assumes you're a developer wanting to introspect a bbop graph directly but there are a wider range of consumers.

will happily help with this, just not sure of yr grand plan. No rush, just noting for the future.

kltm commented 8 years ago

Okay, I see what is going on now.

The main AmiGO graph viewer is tuned to what's loaded in GOlr, allowing people to use shorthands at various levels of detail. It is not a general graph viewer. The formats are similar, but the one you're trying to use uses an historical format, not the general bbop-graph JSON form.

That said, it is backed by a general graph maker. Said viewer has a client in labs, but has not been generally "released": http://tomodachi.berkeleybop.org/visualize?mode=client_freeform If you want, I could pretty easily "graduate" this and add it to 2.5. I think the only outstanding issue is geneontology/amigo#216.

kltm commented 8 years ago

Pinging @cmungall , as current formulation of ticket is invalid. (Not stale as it is a different format entirely.)